InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

By Erik L. L. Sonnhammer, Gabriel Östlund. 2014

452 citations recorded by the source corpus.

The InParanoid database (http://InParanoid.sbc.su.se) provides a user interface to orthologs inferred by the InParanoid algorithm. As there are now international efforts to curate and standardize complete proteomes, we have switched to using these resources rather than gathering and curating the proteomes ourselves. InParanoid release 8 is based on the 66 reference proteomes that the ‘Quest for Orthologs’ community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes—in total 273 species. These represent 246 eukaryotes, 20 bacteria and seven archaea. Compared to the previous release, this increases the number of species by 173% and the number of pairwise species comparisons by 650%. In turn, the number of ortholog groups has increased by 423%. We present the contents and usages of InParanoid 8, and a detailed analysis of how the proteome content has changed since the previous release.

Subfields: Molecular Biology, Spectroscopy

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Citations in the corpus

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces (2017, unknown): “Because orthologs are so important, a large number of methods and resources for their inference have been developed over the years, such as the COGs database (4), Inparanoid (5), OrthoMCL (6), En-sembl Compara (7), KEGG Orthology (8), PhylomeDb (9), OrthoDB (10), EggNOG (11), MBGD (12), PLAZA (13) o”
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species (2015, methodology): “Some of these databases also provide ortholog prediction software (InParanoid: http://software.sbc.su.se/cgi-bin/request.cgi?project=inparanoid, OrthoDB: http://www. orthodb.org/orthodb software/), but generally the software has to be downloaded and run locally.”
Advances and Applications in the Quest for Orthologs (2019, methodology): “…benchmarking service website (https://orthology.benchmarkservice.org; Last accessed April 2019) for nine methods: InParanoid (Sonnhammer and €Ostlund 2015), Hieranoid 2 (Kaduk and Sonnhammer 2017), OMA Groups (Altenhoff et al. 2018), OMA GETHOGs (Altenhoff et al. 2013), OrthoInspector…”